Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.

ABSTRACT: Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often 'called' by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in compa

SUBMITTER: Nordstrom KJV 

PROVIDER: S-EPMC6847574 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature